An Ontology for Bacterial Phenotypes

描述（由申请人提供）：基因组和宏基因组测序工作正在产生大量关于微生物的新信息。表型是由基因型引起的可观察特征，因此是所有生物体生物学的基本方面。我们在基础、应用和临床微生物学中充分利用表型的功能和比较基因组学的能力受到缺乏控制术语来描述和分类的阻碍。本体是具有术语之间定义关系的受控词汇表。该项目的总体目标是建立一个基于本体论的细菌表型注释系统。该项目将开发必要的组件和基础设施，在一个特征良好的模型系统上测试系统，并让相关的科学界参与其开发。组成部分是：1)微生物表型本体（OMP）。2)现有本体的扩展，证据代码本体（ECO），用于描述如何确定OMP表型以及ECO术语与方法资源的交叉引用。3)一个试点项目，使用该系统对大肠杆菌突变的表型进行编目，大肠杆菌是一个很好的细菌模型系统。4)建立一个网站，帮助科学界找到这些细菌表型注释的新资源。5)推广和教育，以促进该系统的使用，并将其纳入遗传学和微生物学的本科和研究生教育。

DESCRIPTION (provided by applicant): Genome and metagenome sequencing efforts are producing a wealth of new information about microbes. Phenotypes are the observable traits resulting from genotypes and thus are a fundamental aspect of the biology of all organisms. Our ability to fully exploit the power of phenotypes for functional and comparative genomics in basic, applied, and clinical microbiology is hindered by the lack of a controlled terminology to describe and classify them. Ontologies are controlled vocabularies with defined relationships between terms. The overall goal of this project is to build a system for ontology-based annotation of bacterial phenotypes. The project will develop the necessary components and infrastructure, test the system on a well-characterized model system, and involve the relevant scientific communities in its development. The components are: 1) an Ontology for Microbial Phenotypes (OMP). 2) An extension of an existing ontology, the Evidence Code Ontology (ECO) to describe how OMP phenotypes were determined and cross referencing of ECO terms to a methods resource. 3) A pilot project to use the system to catalog phenotypes of mutations from E. coli, a well- understood bacterial model system. 4) a web site to help the scientific community find these new resources for bacterial phenotype annotation. 5) Outreach and education to promote the use of the system and to incorporate it into undergraduate and graduate education in genetics and microbiology. PUBLIC HEALTH RELEVANCE: An improved phenotype annotation system will have broad impacts relevant to the mission of NIH. The ability to correlate differences in gene content with important phenotypic differences between strains or microbial communities can help researchers target genes or organisms likely to be involved in virulence, drug resistance, and other important processes to infectious disease and human health. In addition, it can be used to elucidate the function of proteins involved in pathogenesis through comparative analysis based on phenotypes.